Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 96 of 126
Found at i:18753846 original size:15 final size:16
Alignment explanation
Indices: 18753826--18753858 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
18753816 CTTATTTAGT
18753826 TTGGGCCCAAA-TCAA
1 TTGGGCCCAAATTCAA
*
18753841 TTGGGCTCAAATTCAA
1 TTGGGCCCAAATTCAA
18753857 TT
1 TT
18753859 CAACCTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (16 bp):
TTGGGCCCAAATTCAA
Found at i:18755209 original size:57 final size:55
Alignment explanation
Indices: 18755009--18755253 Score: 243
Period size: 54 Copynumber: 4.4 Consensus size: 55
18754999 TTTTTTGAAG
* * *
18755009 AAAAAGTTAAAGTATCAAAATTTTCC-TAAACCAAAAATAATTTCAAAAA-TT-AGA
1 AAAAAGTTGAAGTAT-TAAATTTTCCTTAAA-CAAAAATAATTTAAAAAATTTGAGA
* * * * * *
18755063 AAAAAATAG-AGTTATCAAATTTTCTTTAAACAAAAATAATTTAAAAATTTTTA-A
1 AAAAAGTTGAAG-TATTAAATTTTCCTTAAACAAAAATAATTTAAAAAATTTGAGA
* *
18755117 GAAAAAG-TGAAGTATTAAATTTTTCTTAAATAAAAATAATTTCAAAAAATTTGAGA
1 -AAAAAGTTGAAGTATTAAATTTTCCTTAAACAAAAATAATTT-AAAAAATTTGAGA
* * *
18755173 AAAAAGTTGGAAGTATTAAGTTTTCCTTAAACAAAAAGTAATTTAAAAATTTTTGAGG
1 AAAAAGTT-GAAGTATTAAATTTTCCTTAAACAAAAA-TAATTTAAAAA-ATTTGAGA
18755231 AAAAAGTTGAAGTATT-AATTTTC
1 AAAAAGTTGAAGTATTAAATTTTC
18755254 TTTGAAATTA
Statistics
Matches: 158, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
53 26 0.16
54 43 0.27
55 23 0.15
56 8 0.05
57 38 0.24
58 20 0.13
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (55 bp):
AAAAAGTTGAAGTATTAAATTTTCCTTAAACAAAAATAATTTAAAAAATTTGAGA
Found at i:18763308 original size:52 final size:52
Alignment explanation
Indices: 18763222--18763378 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
18763212 TATAACCATA
* * *
18763222 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
18763274 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * **
18763326 CAAACTTACCTATTAAGAATCATCTTT-CTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-CCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
18763378 C
1 C
18763379 TTCTTGTCCA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 90 0.96
53 4 0.04
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:18763419 original size:11 final size:11
Alignment explanation
Indices: 18763403--18763444 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
18763393 GCAATATCTG
*
18763403 ACAAATCCCAA
1 ACAAATCTCAA
*
18763414 ACAAATCTCTA
1 ACAAATCTCAA
18763425 ACAAATCTCAA
1 ACAAATCTCAA
*
18763436 ACGAATCTC
1 ACAAATCTC
18763445 TTATGGGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:18763428 original size:22 final size:22
Alignment explanation
Indices: 18763403--18763445 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18763393 GCAATATCTG
18763403 ACAAATCCCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
* *
18763425 ACAAATCTCAAACGAATCTCT
1 ACAAATCCCAAACAAATCTCT
18763446 TATGGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:18764355 original size:52 final size:52
Alignment explanation
Indices: 18764269--18764425 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
18764259 TATAACCATA
* * * *
18764269 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
18764321 CAAACTTACCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * **
18764373 CAAACTTACCTATTAAGAATCATCTTT-CTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAATC-CCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
18764425 C
1 C
18764426 TTCTTGTCCA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 90 0.96
53 4 0.04
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:18764466 original size:11 final size:11
Alignment explanation
Indices: 18764450--18764491 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
18764440 GCAATATCTG
*
18764450 ACAAATCCCAA
1 ACAAATCTCAA
*
18764461 ACAAATCTCTA
1 ACAAATCTCAA
18764472 ACAAATCTCAA
1 ACAAATCTCAA
*
18764483 ACGAATCTC
1 ACAAATCTC
18764492 TTATGGGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:18764475 original size:22 final size:22
Alignment explanation
Indices: 18764450--18764492 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18764440 GCAATATCTG
18764450 ACAAATCCCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
* *
18764472 ACAAATCTCAAACGAATCTCT
1 ACAAATCCCAAACAAATCTCT
18764493 TATGGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:18765943 original size:2 final size:2
Alignment explanation
Indices: 18765936--18765963 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18765926 ATTTTACATT
18765936 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18765964 GTAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18766415 original size:29 final size:28
Alignment explanation
Indices: 18766365--18766419 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
18766355 ATTAAAAATA
*
18766365 TATAAAAAATTAAAAATTTAATATTTTAT
1 TATAAAAAATTAAAAATATAAT-TTTTAT
* **
18766394 TATATAAAATTATGAATATAATTTTT
1 TATAAAAAATTAAAAATATAATTTTT
18766420 CATTTTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 4 0.18
29 18 0.82
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TATAAAAAATTAAAAATATAATTTTTAT
Found at i:18767921 original size:3 final size:3
Alignment explanation
Indices: 18767913--18767954 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
18767903 AAGTAACTTG
18767913 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18767955 ATTTTGATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18768563 original size:13 final size:13
Alignment explanation
Indices: 18768545--18768570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18768535 AAATAACTTG
18768545 ATTTTTATTTTTT
1 ATTTTTATTTTTT
18768558 ATTTTTATTTTTT
1 ATTTTTATTTTTT
18768571 CTATAACCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:18769368 original size:22 final size:23
Alignment explanation
Indices: 18769322--18769370 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
18769312 TAAAAAAGTT
** *
18769322 TTTTTTAATATTTAAATTTTTTA
1 TTTTTTAATATTTAAAAATTATA
18769345 TTTTTT-ATATTTAAAAATTATA
1 TTTTTTAATATTTAAAAATTATA
18769367 TTTT
1 TTTT
18769371 AAAACTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTTAATATTTAAAAATTATA
Found at i:18770533 original size:21 final size:22
Alignment explanation
Indices: 18770495--18770537 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
18770485 CTATATATTT
*
18770495 ATATTTGTATTTTTAGAATTAA
1 ATATTTGTATTCTTAGAATTAA
18770517 ATATTTGTA-TCTTAGAATTAA
1 ATATTTGTATTCTTAGAATTAA
18770538 GACAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATATTTGTATTCTTAGAATTAA
Found at i:18770703 original size:26 final size:26
Alignment explanation
Indices: 18770674--18770730 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
18770664 TTTTTCAATA
18770674 TACATTCAGTTTTA-CTCTTAGTTTTT
1 TACATT-AGTTTTATCTCTTAGTTTTT
*
18770700 TACA-TAGTTTTATTTCTTAGTTTTT
1 TACATTAGTTTTATCTCTTAGTTTTT
18770725 TCACAT
1 T-ACAT
18770731 GGTATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.26
25 13 0.48
26 7 0.26
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (26 bp):
TACATTAGTTTTATCTCTTAGTTTTT
Found at i:18770709 original size:24 final size:26
Alignment explanation
Indices: 18770681--18770730 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
18770671 ATATACATTC
18770681 AGTTTTA-CTCTTAGTTTTTT-ACAT
1 AGTTTTATCTCTTAGTTTTTTCACAT
*
18770705 AGTTTTATTTCTTAGTTTTTTCACAT
1 AGTTTTATCTCTTAGTTTTTTCACAT
18770731 GGTATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 12 0.52
26 4 0.17
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (26 bp):
AGTTTTATCTCTTAGTTTTTTCACAT
Found at i:18777999 original size:16 final size:16
Alignment explanation
Indices: 18777978--18778008 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18777968 GTAATTTTTT
18777978 ATTTTTGACTTTGAAA
1 ATTTTTGACTTTGAAA
18777994 ATTTTTGACTTTGAA
1 ATTTTTGACTTTGAA
18778009 GTTAGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (16 bp):
ATTTTTGACTTTGAAA
Found at i:18783336 original size:16 final size:16
Alignment explanation
Indices: 18783306--18783400 Score: 63
Period size: 15 Copynumber: 6.0 Consensus size: 16
18783296 ATGGAAGGTT
*
18783306 TGGGGCTTTGAATTTTA
1 TGGGG-TTTGGATTTTA
18783323 TGGGGTTTGGA-TTTA
1 TGGGGTTTGGATTTTA
* * *
18783338 AGGGATTTTGAATTTTA
1 TGGG-GTTTGGATTTTA
*
18783355 -AGGGTTTCGGATTTT-
1 TGGGGTTT-GGATTTTA
* *
18783370 TGGGTTTTAGATTTTA
1 TGGGGTTTGGATTTTA
*
18783386 -GGGGTTTAGATTTTA
1 TGGGGTTTGGATTTTA
18783401 AGAAAATGTG
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
15 30 0.48
16 23 0.37
17 9 0.15
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (16 bp):
TGGGGTTTGGATTTTA
Found at i:18783353 original size:32 final size:30
Alignment explanation
Indices: 18783312--18783398 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
18783302 GGTTTGGGGC
18783312 TTTGAATTTTATGGGGTTTGGATTTAAGGGAT
1 TTTGAATTTTA-GGGGTTTGGATTTAAGGG-T
* **
18783344 TTTGAATTTTAAGGGTTTCGGATTTTTGGGT
1 TTTGAATTTTAGGGGTTT-GGATTTAAGGGT
*
18783375 TTT-AGATTTTAGGGGTTTAGATTT
1 TTTGA-ATTTTAGGGGTTTGGATTT
18783399 TAAGAAAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 6 0.12
31 22 0.46
32 20 0.42
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.51
Consensus pattern (30 bp):
TTTGAATTTTAGGGGTTTGGATTTAAGGGT
Found at i:18783356 original size:17 final size:16
Alignment explanation
Indices: 18783307--18783358 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
18783297 TGGAAGGTTT
*
18783307 GGGGCTTTGAATTTTAT
1 GGGG-TTTGAATTTTAA
*
18783324 GGGGTTTGGA-TTTAA
1 GGGGTTTGAATTTTAA
*
18783339 GGGATTTTGAATTTTAA
1 GGG-GTTTGAATTTTAA
18783356 GGG
1 GGG
18783359 TTTCGGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.24
16 10 0.34
17 12 0.41
ACGTcount: A:0.21, C:0.02, G:0.35, T:0.42
Consensus pattern (16 bp):
GGGGTTTGAATTTTAA
Found at i:18783382 original size:15 final size:15
Alignment explanation
Indices: 18783317--18783400 Score: 69
Period size: 15 Copynumber: 5.4 Consensus size: 15
18783307 GGGGCTTTGA
*
18783317 ATTTTATGGGGTTTGG
1 ATTTTA-GGGGTTTAG
* * *
18783333 ATTTAAGGGATTTTG
1 ATTTTAGGGGTTTAG
* *
18783348 AATTTTAAGGGTTTCGG
1 -ATTTTAGGGGTTT-AG
* *
18783365 ATTTTTGGGTTTTAG
1 ATTTTAGGGGTTTAG
18783380 ATTTTAGGGGTTTAG
1 ATTTTAGGGGTTTAG
18783395 ATTTTA
1 ATTTTA
18783401 AGAAAATGTG
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
15 27 0.51
16 25 0.47
17 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.50
Consensus pattern (15 bp):
ATTTTAGGGGTTTAG
Found at i:18784794 original size:8 final size:8
Alignment explanation
Indices: 18784781--18784827 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
18784771 TTTGTTTTAA
18784781 TTAATATT
1 TTAATATT
18784789 TTAATAATT
1 TTAAT-ATT
*
18784798 TTGAT-TT
1 TTAATATT
*
18784805 TTAATTTT
1 TTAATATT
18784813 TTAAT-TT
1 TTAATATT
18784820 TTAATATT
1 TTAATATT
18784828 ATTATTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 13 0.38
8 14 0.41
9 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (8 bp):
TTAATATT
Found at i:18784814 original size:15 final size:15
Alignment explanation
Indices: 18784781--18784824 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
18784771 TTTGTTTTAA
*
18784781 TTAATATTTTAATAATT
1 TTAAT-TTTTAAT-TTT
*
18784798 TTGATTTTTAATTTT
1 TTAATTTTTAATTTT
18784813 TTAATTTTTAAT
1 TTAATTTTTAAT
18784825 ATTATTATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTAATTTTTAATTTT
Found at i:18784840 original size:12 final size:12
Alignment explanation
Indices: 18784820--18784864 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
18784810 TTTTTAATTT
18784820 TTAATATTATTA
1 TTAATATTATTA
*
18784832 TTGATATTATTA
1 TTAATATTATTA
*
18784844 TTAAAATTATTA
1 TTAATATTATTA
*
18784856 TTAAAATTA
1 TTAATATTA
18784865 AACTAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
TTAATATTATTA
Found at i:18786227 original size:27 final size:28
Alignment explanation
Indices: 18786187--18786239 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
18786177 AGCACTCTAC
18786187 GTCCCAAAATTTGTGGTGTAGGTGCACT
1 GTCCCAAAATTTGTGGTGTAGGTGCACT
18786215 GTCCC-AAATTTGTGGTGTAGGTGCA
1 GTCCCAAAATTTGTGGTGTAGGTGCA
18786240 TCCTAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (28 bp):
GTCCCAAAATTTGTGGTGTAGGTGCACT
Found at i:18786258 original size:3 final size:3
Alignment explanation
Indices: 18786250--18786305 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
18786240 TCCTAATATG
18786250 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18786298 ATA ATA AT
1 ATA ATA AT
18786306 TTCATGAGAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:18786477 original size:18 final size:20
Alignment explanation
Indices: 18786439--18786482 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
18786429 TTAATAAAAA
*
18786439 AAAATAGATAATAAAATTAT
1 AAAATAGATAATAAAAATAT
18786459 AAAAT-GATAA-AAAAATAT
1 AAAATAGATAATAAAAATAT
18786477 AAAATA
1 AAAATA
18786483 CTTGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 5 0.23
20 5 0.23
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAATAGATAATAAAAATAT
Found at i:18787055 original size:60 final size:60
Alignment explanation
Indices: 18786991--18787109 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
18786981 TATAAAAGGT
*
18786991 AAAATATTATTTAAACAAGATCATTTTAAGATCTTATAAAATTAATTGGTATCGTCTTTA
1 AAAATATTATTTAAACAAGATCATTTTAAGATCTTATAAAATTAATTGATATCGTCTTTA
* * *
18787051 AAAATATTATTTAAATAAGATTATTTTAAGATTTTATAAAATTAATTGATATCGTCTTT
1 AAAATATTATTTAAACAAGATCATTTTAAGATCTTATAAAATTAATTGATATCGTCTTT
18787110 GAAAGAGTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (60 bp):
AAAATATTATTTAAACAAGATCATTTTAAGATCTTATAAAATTAATTGATATCGTCTTTA
Found at i:18788733 original size:2 final size:2
Alignment explanation
Indices: 18788726--18788767 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
18788716 ATTTATTTTG
18788726 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18788768 CACACACCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18791164 original size:53 final size:54
Alignment explanation
Indices: 18791100--18791345 Score: 209
Period size: 53 Copynumber: 4.4 Consensus size: 54
18791090 TAAAAATTTT
18791100 TTTGAAGAAAAAGTTAAAGTATCAAAATTTTCCTAAACCAAAAATAATTTCAAAAA
1 TTTG-AGAAAAAGTTAAAGTATCAAAATTTTCCTAAA-CAAAAATAATTTCAAAAA
** * *
18791156 -TT-AGAAAAAAATAGAGTTATC-AAATTTTCTTTAAACAAAAATAATTT-AAAAA
1 TTTGAGAAAAAGTTAAAG-TATCAAAATTTTC-CTAAACAAAAATAATTTCAAAAA
* * * * *
18791208 TTTTTAAGAAAAAG-TGAAGTAT-TAAATTTTCTTAAATAAAAATAATTTCAAAAAA
1 --TTTGAGAAAAAGTTAAAGTATCAAAATTTTCCTAAACAAAAATAATTTC-AAAAA
* * *
18791263 TTTGAGAAAAAAGTTGAAAGTAT-TAATTTTTCCTTAAACAAAAAATAATTTAAAAAA
1 TTTGAG-AAAAAGTT-AAAGTATCAAAATTTTCC-TAAAC-AAAAATAATTTCAAAAA
*
18791320 TTTTGAGGAAAAAGTTGAAGTATCAA
1 -TTTGA-GAAAAAGTTAAAGTATCAA
18791346 TTTTCTTTGA
Statistics
Matches: 157, Mismatches: 16, Indels: 32
0.77 0.08 0.16
Matches are distributed among these distances:
52 5 0.03
53 52 0.33
54 25 0.16
55 13 0.08
56 21 0.13
57 15 0.10
58 25 0.16
59 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (54 bp):
TTTGAGAAAAAGTTAAAGTATCAAAATTTTCCTAAACAAAAATAATTTCAAAAA
Found at i:18796063 original size:22 final size:20
Alignment explanation
Indices: 18796031--18796074 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
18796021 ACATGTTAAA
18796031 ATTTTGTAATTTATCATATTACT
1 ATTTTGTAA-TTAT-ATA-TACT
18796054 ATTTT-TAATTATATATACT
1 ATTTTGTAATTATATATACT
18796073 AT
1 AT
18796075 ATTGAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 4 0.19
22 3 0.14
23 5 0.24
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTGTAATTATATATACT
Found at i:18800121 original size:24 final size:24
Alignment explanation
Indices: 18800094--18800152 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
18800084 GAAAGCTTTT
*
18800094 AAACCTATGCTAGAAGAGGAAGCA
1 AAACCTATGCTAGAAAAGGAAGCA
18800118 AAACCTATGCTAGAAAAGGAAGCA
1 AAACCTATGCTAGAAAAGGAAGCA
*
18800142 AAACCAATGCT
1 AAACCTATGCT
18800153 GATGAATAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (24 bp):
AAACCTATGCTAGAAAAGGAAGCA
Found at i:18801136 original size:20 final size:20
Alignment explanation
Indices: 18801095--18801137 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18801085 AAATTCAATG
*
18801095 ATTTATTTTGATATTTGCTA
1 ATTTATTTTGATATTTGATA
*
18801115 ATTTATTTTTTATATTT-ATA
1 ATTTA-TTTTGATATTTGATA
18801135 ATT
1 ATT
18801138 GCTAGGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (20 bp):
ATTTATTTTGATATTTGATA
Found at i:18802015 original size:24 final size:25
Alignment explanation
Indices: 18801964--18802021 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
18801954 TAGAATGTTC
18801964 TAAAATTATTTATATTTTTTAATAT
1 TAAAATTATTTATATTTTTTAATAT
*
18801989 TAAAATT-TTT-TATTTTTTATATTT
1 TAAAATTATTTATATTTTTTA-ATAT
18802013 TAAAATTAT
1 TAAAATTAT
18802022 ATTTTAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 9 0.30
24 13 0.43
25 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TAAAATTATTTATATTTTTTAATAT
Found at i:18802021 original size:13 final size:13
Alignment explanation
Indices: 18802005--18802030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18801995 TTTTTATTTT
18802005 TTATATTTTAAAA
1 TTATATTTTAAAA
18802018 TTATATTTTAAAA
1 TTATATTTTAAAA
18802031 CTTTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATATTTTAAAA
Found at i:18802024 original size:22 final size:22
Alignment explanation
Indices: 18801971--18802026 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
18801961 TTCTAAAATT
18801971 ATTTATATTTTTTAATATTAAA
1 ATTTATATTTTTTAATATTAAA
* *
18801993 ATTTTTTATTTTTTATATTTTAAA
1 A-TTTATATTTTTTA-ATATTAAA
18802017 A-TTATATTTT
1 ATTTATATTTT
18802027 AAAACTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.31
23 12 0.41
24 8 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTATATTTTTTAATATTAAA
Found at i:18802057 original size:39 final size:37
Alignment explanation
Indices: 18801988--18802061 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 37
18801978 TTTTTTAATA
* *
18801988 TTAAAATTTTTTATTTTTTATATTTTAAAATTATATT
1 TTAAAATTTTTTATTTTTTATAATTAAAAATTATATT
18802025 TTAAAACTTTTTTAATTTTTTA-ACATTAAAAATTATA
1 TTAAAA-TTTTTT-ATTTTTTATA-ATTAAAAATTATA
18802062 AATGTCTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 6 0.19
38 7 0.22
39 19 0.59
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (37 bp):
TTAAAATTTTTTATTTTTTATAATTAAAAATTATATT
Found at i:18814718 original size:29 final size:28
Alignment explanation
Indices: 18814566--18814718 Score: 92
Period size: 29 Copynumber: 5.3 Consensus size: 28
18814556 TAATTGGTAC
* * *
18814566 TTTAAGTCTAGATTAGCTGGTACTCAAAT
1 TTTAAGCCTAGATTAGCTGGCACT-AGAT
* *
18814595 TTTAAGCTTAGATTAGCTAGCACCTAGAT
1 TTTAAGCCTAGATTAGCTGGCA-CTAGAT
** * * * * *
18814624 TTTAAATCTAAATTAGTTAGCACTTAAAA
1 TTTAAGCCTAGATTAGCTGGCAC-TAGAT
* * * * *
18814653 TTTATG-GTCAGTTTAGTTGGCACCCAGAT
1 TTTAAGCCT-AGATTAGCTGGCA-CTAGAT
18814682 TTTAAGCCTAGATTAGCTGGCATCTAGAT
1 TTTAAGCCTAGATTAGCTGGCA-CTAGAT
18814711 TTTAAGCC
1 TTTAAGCC
18814719 AAGTTTACTA
Statistics
Matches: 92, Mismatches: 27, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
28 2 0.02
29 86 0.93
30 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (28 bp):
TTTAAGCCTAGATTAGCTGGCACTAGAT
Found at i:18816008 original size:22 final size:21
Alignment explanation
Indices: 18815965--18816008 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
18815955 TACTAATATA
* *
18815965 TATTTTTTTATTTTTATCTTT
1 TATTTTTTTATTTTCATATTT
*
18815986 TATTTTATTTATTTTCGTATTT
1 TATTTT-TTTATTTTCATATTT
18816008 T
1 T
18816009 TATATATCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (21 bp):
TATTTTTTTATTTTCATATTT
Found at i:18816927 original size:12 final size:11
Alignment explanation
Indices: 18816905--18817007 Score: 54
Period size: 10 Copynumber: 9.3 Consensus size: 11
18816895 TTTCTTTGAA
18816905 TTTTT-TTTAT
1 TTTTTATTTAT
*
18816915 TTCTTTGTTTAT
1 TT-TTTATTTAT
18816927 TTGTTTATTTTAT
1 TT-TTTA-TTTAT
18816940 TTTTTATTTAT
1 TTTTTATTTAT
**
18816951 TAGATTAGGTTTAT
1 T-TTTTA--TTTAT
* ** *
18816965 GTAATA-TTCT
1 TTTTTATTTAT
18816975 -TTTTATTTA-
1 TTTTTATTTAT
18816984 TTTTTATTTAT
1 TTTTTATTTAT
18816995 TTTTTA-TTAT
1 TTTTTATTTAT
18817005 TTT
1 TTT
18817008 ATTTTCTTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
9 3 0.04
10 23 0.32
11 15 0.21
12 17 0.23
13 10 0.14
14 5 0.07
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:18816989 original size:10 final size:10
Alignment explanation
Indices: 18816974--18817011 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
18816964 TGTAATATTC
18816974 TTTTTATTTA
1 TTTTTATTTA
18816984 TTTTTATTTA
1 TTTTTATTTA
18816994 TTTTT-TATTA
1 TTTTTAT-TTA
18817004 -TTTTATTT
1 TTTTTATTT
18817012 TCTTTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:18816995 original size:14 final size:15
Alignment explanation
Indices: 18816975--18817012 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
18816965 GTAATATTCT
18816975 TTTTATTTATTT-TTA
1 TTTTATTT-TTTATTA
18816990 -TTTATTTTTTATTA
1 TTTTATTTTTTATTA
18817004 TTTTATTTT
1 TTTTATTTT
18817013 CTTTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.14
14 10 0.48
15 8 0.38
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTTTTTATTA
Found at i:18817010 original size:25 final size:26
Alignment explanation
Indices: 18816908--18817012 Score: 69
Period size: 25 Copynumber: 4.2 Consensus size: 26
18816898 CTTTGAATTT
* *
18816908 TTTTTATTTCTTTGTTTATT-TGTTTA
1 TTTTTATTTATTTATTTATTAT-TTTA
**
18816934 -TTTTATTT-TTTATTTATTAGATTA
1 TTTTTATTTATTTATTTATTATTTTA
** * *
18816958 GGTTTATGTAATATTCTTT-TTA-TTTA
1 TTTTTAT-TTAT-TTATTTATTATTTTA
18816984 TTTTTATTTATTT-TTTATTATTTTA
1 TTTTTATTTATTTATTTATTATTTTA
18817009 TTTT
1 TTTT
18817013 CTTTAAATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
23 3 0.05
24 17 0.27
25 24 0.39
26 9 0.15
27 4 0.06
28 5 0.08
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (26 bp):
TTTTTATTTATTTATTTATTATTTTA
Found at i:18817101 original size:59 final size:59
Alignment explanation
Indices: 18817038--18817377 Score: 453
Period size: 59 Copynumber: 5.7 Consensus size: 59
18817028 AAAAATTCAA
*
18817038 AAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
*
18817097 --AAAAAATATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTC
1 AAAAAAAATATTTTTAGGG-AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
*
18817153 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTTC
* *
18817217 AAAAAAAATAATTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
***
18817276 AAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTTC
1 AAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTTC
*
18817337 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
18817378 CTACAAAAAA
Statistics
Matches: 252, Mismatches: 14, Indels: 30
0.85 0.05 0.10
Matches are distributed among these distances:
56 6 0.02
57 47 0.19
58 40 0.16
59 93 0.37
60 1 0.00
61 12 0.05
63 7 0.03
64 46 0.18
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.34
Consensus pattern (59 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
Found at i:18818334 original size:113 final size:112
Alignment explanation
Indices: 18818133--18818337 Score: 268
Period size: 113 Copynumber: 1.8 Consensus size: 112
18818123 TTTTTTTCAA
* * * * *
18818133 AATTCTCGATGGTAATATCCGAGTTTTTTCAAAATTATTTAATGGTGATATTCAAGTATTAAAGT
1 AATTCTCAATGGTAATATCCAAGTTTTTTCAAAATCACTCAATGGTGATATTCAAGTATTAAAGT
* * * *
18818198 TTGAATTTTATTTTTATGATGGTGATATCTAGGCCCTTTCATTAAAT
66 CTAAATTTCATTTTTATCATGGTGATATCTAGGCCCTTTCATTAAAT
* * * *
18818245 AATTCTCAATGGTCATATTCAAGTTTCTTTCAAAATCACTCGATGGTGATATTCGAGTATTAAAG
1 AATTCTCAATGGTAATATCCAAGTTT-TTTCAAAATCACTCAATGGTGATATTCAAGTATTAAAG
18818310 TCTAAATTTCATTTTT-TCAGTGGTGATA
65 TCTAAATTTCATTTTTATCA-TGGTGATA
18818338 ACTGAGCTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
112 24 0.31
113 54 0.69
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (112 bp):
AATTCTCAATGGTAATATCCAAGTTTTTTCAAAATCACTCAATGGTGATATTCAAGTATTAAAGT
CTAAATTTCATTTTTATCATGGTGATATCTAGGCCCTTTCATTAAAT
Found at i:18820300 original size:13 final size:13
Alignment explanation
Indices: 18820284--18820309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18820274 AATTCAAAAC
18820284 AAAATAAAAAATA
1 AAAATAAAAAATA
18820297 AAAATAAAAAATA
1 AAAATAAAAAATA
18820310 GCTGAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:18821014 original size:17 final size:16
Alignment explanation
Indices: 18820964--18821014 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
18820954 GAAAAATTGA
*
18820964 TATTTTTTATTTTTTCT
1 TATTTTTTATTTATT-T
*
18820981 TA-TTTTTAATTATTT
1 TATTTTTTATTTATTT
18820996 TATTTATTTATTTATTT
1 TATTT-TTTATTTATTT
18821013 TA
1 TA
18821015 CAATTTAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
17 14 0.48
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTTTTATTTATTT
Found at i:18821105 original size:7 final size:7
Alignment explanation
Indices: 18821079--18821115 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
18821069 TTGAATAATG
18821079 AATAAAT
1 AATAAAT
18821086 AA-AAAT
1 AATAAAT
18821092 AAATAAAT
1 -AATAAAT
18821100 AATAAAT
1 AATAAAT
18821107 AATAAAT
1 AATAAAT
18821114 AA
1 AA
18821116 AATGATGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 4 0.14
7 20 0.71
8 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:18821238 original size:3 final size:3
Alignment explanation
Indices: 18821230--18821272 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
18821220 TTTCAAACAT
*
18821230 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18821273 CAACAACAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:18821347 original size:3 final size:3
Alignment explanation
Indices: 18821339--18821384 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
18821329 AGAAAAAGAG
18821339 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18821385 CTCTTGGGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18822006 original size:11 final size:12
Alignment explanation
Indices: 18821990--18822018 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
18821980 TTTAATATTG
18821990 AAAATAATAA-T
1 AAAATAATAAGT
18822001 AAAATAATAAGT
1 AAAATAATAAGT
18822013 AAAATA
1 AAAATA
18822019 CTATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AAAATAATAAGT
Found at i:18822459 original size:17 final size:17
Alignment explanation
Indices: 18822432--18822464 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
18822422 AAAATTGAAT
18822432 ATTTTATAAC-ATAAAG
1 ATTTTATAACAATAAAG
18822448 ATTTTAATAACAATAAA
1 ATTTT-ATAACAATAAA
18822465 ATAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTTTATAACAATAAAG
Found at i:18823148 original size:15 final size:16
Alignment explanation
Indices: 18823112--18823150 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
18823102 ATGCAAATTG
* *
18823112 AATCTTAATTTTGTAT
1 AATCTTAATTTTGCAA
18823128 AATCTTAATTTT-CAA
1 AATCTTAATTTTGCAA
18823143 AATCTTAA
1 AATCTTAA
18823151 AACAAGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (16 bp):
AATCTTAATTTTGCAA
Found at i:18825917 original size:7 final size:8
Alignment explanation
Indices: 18825886--18825916 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
18825876 TCCAATTGGC
18825886 AAAAAAAGG
1 AAAAAAA-G
18825895 AAAAAAAG
1 AAAAAAAG
18825903 AAAAAAAG
1 AAAAAAAG
18825911 AAAAAA
1 AAAAAA
18825917 GGGCTACTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:18830542 original size:20 final size:19
Alignment explanation
Indices: 18830504--18830559 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
18830494 TTTTAGTCAG
*
18830504 TAAAATTCATCAATCATAA
1 TAAAATTCATCAATAATAA
*
18830523 TAAAATTCCTTCAATAATAA
1 TAAAATT-CATCAATAATAA
* *
18830543 TCAAATTTCATCGATAA
1 T-AAAATTCATCAATAA
18830560 AATCCATTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 7 0.23
20 18 0.60
21 5 0.17
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAATTCATCAATAATAA
Found at i:18830811 original size:21 final size:21
Alignment explanation
Indices: 18830787--18830832 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
18830777 TATAATACTA
*
18830787 AAAAATA-TTCATAACATCCAT
1 AAAAATACTT-ATAACATCCAC
*
18830808 AAAAATACTTATAATATCCAC
1 AAAAATACTTATAACATCCAC
18830829 AAAA
1 AAAA
18830833 GTCTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAATACTTATAACATCCAC
Found at i:18833283 original size:3 final size:3
Alignment explanation
Indices: 18833275--18833333 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
18833265 CTCATTTGTT
* ** ** *
18833275 TCA TCA TCA TTA TCA TCA TCA TCA TTTT TTT TCA TCA TAA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA -TCA TCA TCA TCA TCA TCA TCA
18833321 TCA TCA TCA TCA T
1 TCA TCA TCA TCA T
18833334 TTTTTTGGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 46 0.98
4 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (3 bp):
TCA
Found at i:18833324 original size:34 final size:34
Alignment explanation
Indices: 18833275--18833339 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
18833265 CTCATTTGTT
* *
18833275 TCATCATCATTATCATCATCATCATTTTTTTTCA
1 TCATAATCATCATCATCATCATCATTTTTTTTCA
18833309 TCATAATCATCATCATCATCATCATTTTTTT
1 TCATAATCATCATCATCATCATCATTTTTTT
18833340 GGTTTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (34 bp):
TCATAATCATCATCATCATCATCATTTTTTTTCA
Found at i:18837034 original size:17 final size:17
Alignment explanation
Indices: 18837012--18837045 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18837002 ACACATGCAT
18837012 CACATATGTCATAAAGG
1 CACATATGTCATAAAGG
18837029 CACATATGTCATAAAGG
1 CACATATGTCATAAAGG
18837046 TAATTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (17 bp):
CACATATGTCATAAAGG
Found at i:18838194 original size:20 final size:21
Alignment explanation
Indices: 18838167--18838214 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
18838157 ACGAGGAGCG
* *
18838167 GAGAGAAAGGAAGAGATGAGA
1 GAGAGAAAAGAAGAGAGGAGA
*
18838188 G-GAGAAAAGAGGAGAGGAGA
1 GAGAGAAAAGAAGAGAGGAGA
18838208 GAGAGAA
1 GAGAGAA
18838215 GGTGAGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (21 bp):
GAGAGAAAAGAAGAGAGGAGA
Found at i:18840963 original size:31 final size:30
Alignment explanation
Indices: 18840928--18841005 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 30
18840918 TTATTATTAT
*
18840928 TTTATTTTTTATTTTATGTA-TATCTTATATA
1 TTTATTTTTTATTTTAT-TATTA-CTAATATA
* *
18840959 TTTATTATTTA-CTTATTATTACTAATATA
1 TTTATTTTTTATTTTATTATTACTAATATA
18840988 -TT-TTTTTTATTTT-TTATT
1 TTTATTTTTTATTTTATTATT
18841006 TTATTTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
27 11 0.28
28 4 0.10
29 9 0.22
30 6 0.15
31 10 0.25
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (30 bp):
TTTATTTTTTATTTTATTATTACTAATATA
Found at i:18841007 original size:16 final size:16
Alignment explanation
Indices: 18840918--18841016 Score: 58
Period size: 16 Copynumber: 6.0 Consensus size: 16
18840908 TGTATCTTGA
18840918 TTATTATTATTTTATTTT
1 TTATT-TTA-TTTATTTT
* * *
18840936 TTATTTTATGTATATC
1 TTATTTTATTTATTTT
* *
18840952 TTA-TATATTTATTAT
1 TTATTTTATTTATTTT
**
18840967 TTACTTATTA-TTACTAAT
1 TTA-TT-TTATTTA-TTTT
* *
18840985 ATATTTTTTTTATTTT
1 TTATTTTATTTATTTT
18841001 TTATTTTATTTATTTT
1 TTATTTTATTTATTTT
18841017 CGTATTTTTA
Statistics
Matches: 60, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
15 10 0.17
16 26 0.43
17 12 0.20
18 12 0.20
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (16 bp):
TTATTTTATTTATTTT
Found at i:18841048 original size:24 final size:23
Alignment explanation
Indices: 18841021--18841071 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
18841011 TATTTTCGTA
** *
18841021 TTTTTATATATCTGATATTATTC
1 TTTTTATATATCCCATAATATTC
* *
18841044 TTTTTATTTATCCCATAATATTT
1 TTTTTATATATCCCATAATATTC
18841067 TTTTT
1 TTTTT
18841072 TATTTATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTATATATCCCATAATATTC
Found at i:18841546 original size:19 final size:20
Alignment explanation
Indices: 18841522--18841560 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
18841512 TTCGGCCAAC
18841522 TTCCGGCGA-AATTTCCAGA
1 TTCCGGCGACAATTTCCAGA
* *
18841541 TTCCGGTGACATTTTCCAGA
1 TTCCGGCGACAATTTCCAGA
18841561 ATTCGACACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (20 bp):
TTCCGGCGACAATTTCCAGA
Found at i:18841924 original size:23 final size:21
Alignment explanation
Indices: 18841894--18841948 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
18841884 TCCAGGTTTT
18841894 TTTTTTTTTTTTCTTTCTTTGAA
1 TTTTTTTTTTTTCTTTCTTT--A
* *
18841917 TTTTTTTTATTTCTTTGTTTA
1 TTTTTTTTTTTTCTTTCTTTA
*
18841938 TTTTATTTTTT
1 TTTTTTTTTTT
18841949 ATTTATTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 10 0.36
23 18 0.64
ACGTcount: A:0.09, C:0.05, G:0.04, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTTTTCTTTCTTTA
Found at i:18841941 original size:19 final size:19
Alignment explanation
Indices: 18841898--18841945 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
18841888 GGTTTTTTTT
*
18841898 TTTTTTTTCTTTCTTTGAA
1 TTTTTTTTATTTCTTTGAA
18841917 TTTTTTTTATTTCTTTG--
1 TTTTTTTTATTTCTTTGAA
*
18841934 TTTATTTTATTT
1 TTTTTTTTATTT
18841946 TTTATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 11 0.41
19 16 0.59
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTTTTTTATTTCTTTGAA
Found at i:18842160 original size:116 final size:116
Alignment explanation
Indices: 18842023--18842423 Score: 594
Period size: 116 Copynumber: 3.4 Consensus size: 116
18842013 ATAAAAATAA
18842023 AAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
1 AAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
18842088 CCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
66 CCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
18842139 -AAATTTCGAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAAT
1 AAAATTTC-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAAT
*
18842202 TTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAAT
64 TTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
* * *
18842255 AAAATTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAATT
1 AAAATTTC-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATT
* * *
18842320 TTCAAAAAA-AGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT-TGAAAAT
65 TCCAAAAAATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAAT
* * * * *
18842374 CGAAATTTCCAAAAAAATATTTTTGGGGAAAAGCTGAAAGTATTAATTTT
1 -AAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
18842424 TCCTACAAAA
Statistics
Matches: 262, Mismatches: 14, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
115 8 0.03
116 106 0.40
117 66 0.25
118 2 0.01
119 74 0.28
120 6 0.02
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (116 bp):
AAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
CCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
Found at i:18842182 original size:59 final size:58
Alignment explanation
Indices: 18842024--18842423 Score: 556
Period size: 59 Copynumber: 6.8 Consensus size: 58
18842014 TAAAAATAAA
*
18842024 AAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
18842082 AAATTTC-CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
1 AAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*
18842139 AAATTTCGAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAAT
1 AAATTTC-AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AAT
* * *
18842198 AAATTTC-CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAAT
1 AAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
18842255 AAAATTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAAT
1 -AAATTTC-AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*** *
18842315 AAATTTTCAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT
1 AAA-TTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT
* * *
18842374 CGAAATTTCCAAAAAAATATTTTTGGGGAAAAGCTGAAAGTATTAATTTT
1 --AAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
18842424 TCCTACAAAA
Statistics
Matches: 305, Mismatches: 26, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
57 98 0.32
58 16 0.05
59 99 0.32
60 89 0.29
61 3 0.01
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (58 bp):
AAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:18842281 original size:60 final size:59
Alignment explanation
Indices: 18842024--18842423 Score: 564
Period size: 57 Copynumber: 6.8 Consensus size: 59
18842014 TAAAAATAAA
*
18842024 AAATTT-CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTCCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*
18842082 AAATTTCC--AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
1 AAATTTCCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
18842139 AAATTTCGAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAAT
1 AAATTTCCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AAT
* *
18842198 AAATTTCC--AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAAT
1 AAATTTCCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
18842255 AAAATTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAAT
1 AAATTTCC-AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *** *
18842315 AAATTTTCAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT
1 AAATTTCCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT
* *
18842374 CGAAATTTCC-AAAAAAATATTTTTGGGGAAAAGCTGAAAGTATTAATTTT
1 --AAATTTCCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
18842424 TCCTACAAAA
Statistics
Matches: 306, Mismatches: 25, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
57 105 0.34
58 9 0.03
59 97 0.32
60 88 0.29
61 7 0.02
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (59 bp):
AAATTTCCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:18847733 original size:3 final size:3
Alignment explanation
Indices: 18847725--18847749 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18847715 ACCGAATGTT
18847725 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
18847750 TAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:18850608 original size:3 final size:3
Alignment explanation
Indices: 18850602--18850635 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
18850592 AATTGAGTAG
18850602 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
18850636 TTTATGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:18851316 original size:14 final size:14
Alignment explanation
Indices: 18851297--18851334 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
18851287 TAATATTCAA
*
18851297 AATAATTAAATAAT
1 AATAATAAAATAAT
18851311 AATAATAAAATAAT
1 AATAATAAAATAAT
18851325 -A-AATAAAATA
1 AATAATAAAATA
18851335 CTATTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.39
13 1 0.04
14 13 0.57
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:18851954 original size:8 final size:8
Alignment explanation
Indices: 18851937--18851966 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
18851927 GCTTAGTGAG
18851937 AAAAAGAA
1 AAAAAGAA
*
18851945 AAAAAAAA
1 AAAAAGAA
18851953 AAAAAGAA
1 AAAAAGAA
18851961 AAAAAG
1 AAAAAG
18851967 GAGTGCTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:18852059 original size:2 final size:2
Alignment explanation
Indices: 18852052--18852083 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18852042 TAAAATAAAA
18852052 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18852084 AAAATAGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18855191 original size:14 final size:13
Alignment explanation
Indices: 18855163--18855187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18855153 ATTTTTTAAG
18855163 TTCTTTTCATTTA
1 TTCTTTTCATTTA
18855176 TTCTTTTCATTT
1 TTCTTTTCATTT
18855188 TATTTATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTTTCATTTA
Found at i:18855286 original size:12 final size:13
Alignment explanation
Indices: 18855269--18855297 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18855259 AACAATTTTT
18855269 AAAAAATT-GGGA
1 AAAAAATTAGGGA
18855281 AAAAAATTAGGGA
1 AAAAAATTAGGGA
18855294 AAAA
1 AAAA
18855298 GTTAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (13 bp):
AAAAAATTAGGGA
Found at i:18855646 original size:57 final size:57
Alignment explanation
Indices: 18855456--18855817 Score: 212
Period size: 57 Copynumber: 6.5 Consensus size: 57
18855446 TTTTTTGAAG
* * ** * *
18855456 AAAAAGTTAAAGTGTCAAATTTT-TCTTAAA-CCAAAAATAATTTCAAAAA--TTAGGA
1 AAAAAGTTGAAGTATCAAATTTTCT-TTAAATAAAAAAAT-ATTTTAAAAATTTTGGGA
* * * * * * *
18855511 AAAAAATAGAATTATCAAA-TTTCTTTAAACAAGAATA-ATTTT-AAAATTTTAAGGA
1 AAAAAGTTGAAGTATCAAATTTTCTTTAAATAAAAAAATATTTTAAAAATTTT-GGGA
* * *
18855566 AAAAAGTTGATGTAT-AATTTTTTCTTTAAATAAAAAAATATTTTAAAAATTTTGGGG
1 AAAAAGTTGAAGTATCAA-ATTTTCTTTAAATAAAAAAATATTTTAAAAATTTTGGGA
* * * * ** * *
18855623 AAAAAGTTAAAATATCAAATTTTCATT-GACCAAAAAATAATTTT-AAAATTTTTGAA
1 AAAAAGTTGAAGTATCAAATTTTCTTTAAATAAAAAAAT-ATTTTAAAAATTTTGGGA
* * * * * *
18855679 AAAAAG-TGAAGTATCAAATTTTCCTTAAATAAAAATA-ATGTCAAAAAATTTGAGA
1 AAAAAGTTGAAGTATCAAATTTTCTTTAAATAAAAAAATATTTTAAAAATTTTGGGA
* * * * **
18855734 AAAAAATTGGAAGTATCAATTTTTCTTTAAA-CAAAAAATAATTTAAAAATTTTTAAAGA
1 AAAAAGTT-GAAGTATCAAATTTTCTTTAAATAAAAAAATATTTTAAAAA-TTTT-GGGA
* *
18855793 AAAAA-TTGATGTATCAATTTTTCTT
1 AAAAAGTTGAAGTATCAAATTTTCTT
18855818 GAATTTAAAT
Statistics
Matches: 234, Mismatches: 55, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
52 4 0.02
53 4 0.02
54 15 0.06
55 63 0.27
56 50 0.21
57 75 0.32
58 15 0.06
59 8 0.03
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.36
Consensus pattern (57 bp):
AAAAAGTTGAAGTATCAAATTTTCTTTAAATAAAAAAATATTTTAAAAATTTTGGGA
Found at i:18855707 original size:112 final size:112
Alignment explanation
Indices: 18855473--18855815 Score: 306
Period size: 112 Copynumber: 3.1 Consensus size: 112
18855463 TAAAGTGTCA
* * * * * *
18855473 AATTTTT-CTTAAACCAAAAATAATTTC-AAAAATTAG-GAAAAAAATAG-AATTATCAAA-TTT
1 AATTTTTCCTTAAA-TAAAAAAAATGTCAAAAAATTTGAGAAAAAAATTGAAAATATCAAATTTT
* * * *
18855533 CTTTAAAC-AAGAATAATTTTAAAATTTTAAGGAAAAAAGTTGATGTAT-
65 CATTAAACAAAAAATAATTTTAAAATTTT-TGAAAAAAAG-TGATGTATC
* * * * * * *
18855581 AATTTTTTCTTTAAATAAAAAAATATTTTAAAAATTTTGGGGAAAAAGTT-AAAATATCAAATTT
1 AA-TTTTTCCTTAAATAAAAAAA-ATGTCAAAAAATTTGAGAAAAAAATTGAAAATATCAAATTT
* * *
18855645 TCATTGACCAAAAAATAATTTTAAAATTTTTGAAAAAAAGTGAAGTATC
64 TCATTAAACAAAAAATAATTTTAAAATTTTTGAAAAAAAGTGATGTATC
* * * * *
18855694 AAATTTTCCTTAAATAAAAATAATGTCAAAAAATTTGAGAAAAAAATTGGAAGTATCAATTTTTC
1 AATTTTTCCTTAAATAAAAAAAATGTCAAAAAATTTGAGAAAAAAATTGAAAATATCAAATTTTC
* * * *
18855759 TTTAAACAAAAAATAATTTAAAAATTTTTAAAGAAAAAATTGATGTATC
66 ATTAAACAAAAAATAATTTTAAAATTTTT-GA-AAAAAAGTGATGTATC
18855808 AATTTTTC
1 AATTTTTC
18855816 TTGAATTTAA
Statistics
Matches: 186, Mismatches: 37, Indels: 18
0.77 0.15 0.07
Matches are distributed among these distances:
108 2 0.01
109 11 0.06
110 9 0.05
111 27 0.15
112 78 0.42
113 19 0.10
114 40 0.22
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (112 bp):
AATTTTTCCTTAAATAAAAAAAATGTCAAAAAATTTGAGAAAAAAATTGAAAATATCAAATTTTC
ATTAAACAAAAAATAATTTTAAAATTTTTGAAAAAAAGTGATGTATC
Found at i:18856846 original size:20 final size:21
Alignment explanation
Indices: 18856816--18856882 Score: 84
Period size: 20 Copynumber: 3.3 Consensus size: 21
18856806 CTTGTATATT
18856816 CATAAACATGCATATATACTA
1 CATAAACATGCATATATACTA
* * *
18856837 CATAAA-ATGCTTGTATA-TT
1 CATAAACATGCATATATACTA
*
18856856 CATAAACATGCATATGTACTA
1 CATAAACATGCATATATACTA
18856877 CATAAA
1 CATAAA
18856883 AGCTTTCATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 7 0.19
20 17 0.46
21 13 0.35
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (21 bp):
CATAAACATGCATATATACTA
Found at i:18856859 original size:40 final size:40
Alignment explanation
Indices: 18856804--18856887 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
18856794 GCAATTTCAT
18856804 TGCTTGTATATTCATAAACATGCATATATACTACATAAAA
1 TGCTTGTATATTCATAAACATGCATATATACTACATAAAA
*
18856844 TGCTTGTATATTCATAAACATGCATATGTACTACATAAAA
1 TGCTTGTATATTCATAAACATGCATATATACTACATAAAA
18856884 -GCTT
1 TGCTT
18856888 TCATAAAACC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (40 bp):
TGCTTGTATATTCATAAACATGCATATATACTACATAAAA
Found at i:18856873 original size:22 final size:22
Alignment explanation
Indices: 18856808--18856873 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 22
18856798 TTTCATTGCT
18856808 TGTATATTCATAAACATGCATA
1 TGTATATTCATAAACATGCATA
*
18856830 --TATACTACATAAA-ATGC-T-
1 TGTATA-TTCATAAACATGCATA
18856848 TGTATATTCATAAACATGCATA
1 TGTATATTCATAAACATGCATA
18856870 TGTA
1 TGTA
18856874 CTACATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
19 8 0.22
20 16 0.44
21 8 0.22
22 4 0.11
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
TGTATATTCATAAACATGCATA
Found at i:18860894 original size:22 final size:23
Alignment explanation
Indices: 18860848--18860896 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
18860838 TAAAAAAGTT
** *
18860848 TTTTTTAATATTTAAATTTTTTA
1 TTTTTTAATATTTAAAAATTATA
18860871 TTTTTT-ATATTTAAAAATTATA
1 TTTTTTAATATTTAAAAATTATA
18860893 TTTT
1 TTTT
18860897 AAAACTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTTAATATTTAAAAATTATA
Found at i:18862045 original size:22 final size:22
Alignment explanation
Indices: 18862020--18862063 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18862010 CTATATATTT
*
18862020 ATATTTGTATTTTTAGAATTAA
1 ATATTTGTATCTTTAGAATTAA
18862042 ATATTTGTATCTTTAGAATTAA
1 ATATTTGTATCTTTAGAATTAA
18862064 GGACAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (22 bp):
ATATTTGTATCTTTAGAATTAA
Found at i:18862230 original size:26 final size:26
Alignment explanation
Indices: 18862201--18862257 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
18862191 TTTTTCAGTA
18862201 TACATTCAGTTTTA-CTCTTAGTTTTT
1 TACATT-AGTTTTATCTCTTAGTTTTT
*
18862227 TACA-TAGTTTTATTTCTTAGTTTTT
1 TACATTAGTTTTATCTCTTAGTTTTT
18862252 TCACAT
1 T-ACAT
18862258 GGTATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.26
25 13 0.48
26 7 0.26
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (26 bp):
TACATTAGTTTTATCTCTTAGTTTTT
Found at i:18862236 original size:24 final size:26
Alignment explanation
Indices: 18862208--18862257 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
18862198 GTATACATTC
18862208 AGTTTTA-CTCTTAGTTTTTT-ACAT
1 AGTTTTATCTCTTAGTTTTTTCACAT
*
18862232 AGTTTTATTTCTTAGTTTTTTCACAT
1 AGTTTTATCTCTTAGTTTTTTCACAT
18862258 GGTATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 12 0.52
26 4 0.17
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (26 bp):
AGTTTTATCTCTTAGTTTTTTCACAT
Found at i:18874306 original size:17 final size:17
Alignment explanation
Indices: 18874284--18874316 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18874274 GCTATTATTA
18874284 ATTCAACCTTTT-TCTTG
1 ATTCAA-CTTTTCTCTTG
18874301 ATTCAACTTTTCTCTT
1 ATTCAACTTTTCTCTT
18874317 CAACCATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTCAACTTTTCTCTTG
Found at i:18876573 original size:1 final size:1
Alignment explanation
Indices: 18876567--18876604 Score: 67
Period size: 1 Copynumber: 38.0 Consensus size: 1
18876557 TGATATAAGC
*
18876567 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18876605 CATGCCAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:18879694 original size:2 final size:2
Alignment explanation
Indices: 18879689--18879713 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18879679 TGAATGCTAC
18879689 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18879714 AAACCTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18883461 original size:15 final size:15
Alignment explanation
Indices: 18883433--18883488 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
18883423 TTAATAAAAA
*
18883433 TAATATAATATAATTT
1 TAAT-TAATTTAATTT
18883449 TAATTAATTTAATTT
1 TAATTAATTTAATTT
*
18883464 TAAATAATTTAATTT
1 TAATTAATTTAATTT
*
18883479 AAAATTAATT
1 -TAATTAATT
18883489 AAACCGACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 24 0.69
16 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTAATTTAATTT
Found at i:18889730 original size:15 final size:18
Alignment explanation
Indices: 18889696--18889734 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
18889686 AAAAAATGAA
18889696 AAAATTATAAATTAATTT
1 AAAATTATAAATTAATTT
18889714 AAAATTAT-AA-T-ATTT
1 AAAATTATAAATTAATTT
18889729 AAAATT
1 AAAATT
18889735 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 1 0.05
17 2 0.10
18 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTATAAATTAATTT
Found at i:18889848 original size:18 final size:19
Alignment explanation
Indices: 18889811--18889852 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
18889801 TTAAATCGAA
* *
18889811 TTATTTATTTTTATAGATT
1 TTATATATTTTTATAAATT
18889830 TTATATATTTTT-TAAATT
1 TTATATATTTTTATAAATT
18889848 TTATA
1 TTATA
18889853 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATATTTTTATAAATT
Found at i:18889931 original size:17 final size:18
Alignment explanation
Indices: 18889909--18889948 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
18889899 AAAATAATAT
18889909 ATAAAA-ATTAAAAATCA
1 ATAAAATATTAAAAATCA
*
18889926 ATAAAATTTTAAAAATCA
1 ATAAAATATTAAAAATCA
18889944 ATAAA
1 ATAAA
18889949 TCAAACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAATATTAAAAATCA
Found at i:18891927 original size:19 final size:18
Alignment explanation
Indices: 18891905--18891968 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
18891895 GAAATTAATT
18891905 TAATAATTTTAATTTAAAA
1 TAAT-ATTTTAATTTAAAA
18891924 TAATA-TTT-A--TAAAA
1 TAATATTTTAATTTAAAA
*
18891938 TAATATTTTTAATAT-AAA
1 TAATA-TTTTAATTTAAAA
*
18891956 TTATATTTTAATT
1 TAATATTTTAATT
18891969 ATACATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
14 10 0.26
16 4 0.11
17 11 0.29
18 8 0.21
19 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATATTTTAATTTAAAA
Found at i:18891936 original size:14 final size:14
Alignment explanation
Indices: 18891919--18891945 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18891909 AATTTTAATT
18891919 TAAAATAATATTTA
1 TAAAATAATATTTA
18891933 TAAAATAATATTT
1 TAAAATAATATTT
18891946 TTAATATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAATAATATTTA
Found at i:18891971 original size:18 final size:19
Alignment explanation
Indices: 18891930--18891976 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
18891920 AAAATAATAT
18891930 TTATAAAATAATATTTTTAA
1 TTAT-AAATAATATTTTTAA
*
18891950 -TATAAATTATA-TTTTAA
1 TTATAAATAATATTTTTAA
*
18891967 TTATACATAA
1 TTATAAATAA
18891977 ATATAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 6 0.26
18 14 0.61
19 3 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATAAATAATATTTTTAA
Found at i:18892011 original size:42 final size:41
Alignment explanation
Indices: 18891932--18892040 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 41
18891922 AATAATATTT
18891932 ATAAAATAATATTTTTAATATAAATTATATTTTAATTATAC
1 ATAAAATAATATTTTTAATATAAATTATATTTTAATTATAC
* * *
18891973 ATAAATATAATATTTTT-AT-TAAGTTAATATTTTAAATTAAATT
1 ATAAA-ATAATATTTTTAATATAAATT-ATATTTT-AATTATA-C
*
18892016 ATTAAATAATAATTTATTAATATAA
1 ATAAAATAAT-ATTT-TTAATATAA
18892041 TACATATATA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
40 5 0.09
41 14 0.25
42 22 0.39
43 8 0.14
44 2 0.04
45 2 0.04
46 3 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (41 bp):
ATAAAATAATATTTTTAATATAAATTATATTTTAATTATAC
Found at i:18892056 original size:17 final size:16
Alignment explanation
Indices: 18892021--18892075 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
18892011 AAATTATTAA
* *
18892021 ATAATAATTTATTAAT
1 ATAATAATATATAAAT
18892037 ATAATACATATATAAAT
1 ATAATA-ATATATAAAT
*
18892054 ATAA-AATTAAATAAA-
1 ATAATAA-TATATAAAT
18892069 ATAATAA
1 ATAATAA
18892076 AATAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.15
16 16 0.48
17 12 0.36
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAATATATAAAT
Found at i:18893554 original size:15 final size:14
Alignment explanation
Indices: 18893529--18893559 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
18893519 GAGATTTTAT
18893529 ATTAATTTAAATTA
1 ATTAATTTAAATTA
18893543 ATTAATTTTAAATTA
1 ATTAA-TTTAAATTA
18893558 AT
1 AT
18893560 GGCATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTAATTTAAATTA
Found at i:18893885 original size:27 final size:27
Alignment explanation
Indices: 18893855--18893935 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 27
18893845 TTAGATATAA
*
18893855 TTTTTT-AAAAATAATTGTATGAATTT
1 TTTTTTAAAAAATAATTATATGAATTT
* *
18893881 TTTTTATAAAAAAAGAATTATATAAATTT
1 TTTTT-T-AAAAAATAATTATATGAATTT
* *
18893910 TTTATAAAAAAATAATTATATGAATT
1 TTTTTTAAAAAATAATTATATGAATT
18893936 AATTAGGTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
26 5 0.11
27 19 0.42
29 21 0.47
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (27 bp):
TTTTTTAAAAAATAATTATATGAATTT
Found at i:18893908 original size:29 final size:29
Alignment explanation
Indices: 18893861--18893935 Score: 109
Period size: 27 Copynumber: 2.7 Consensus size: 29
18893851 ATAATTTTTT
*
18893861 AAAAATAATTGTATGAATTTTTTTTATAA
1 AAAAATAATTATATGAATTTTTTTTATAA
* *
18893890 AAAAAGAATTATAT-AA-ATTTTTTATAA
1 AAAAATAATTATATGAATTTTTTTTATAA
18893917 AAAAATAATTATATGAATT
1 AAAAATAATTATATGAATT
18893936 AATTAGGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 23 0.59
28 4 0.10
29 12 0.31
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (29 bp):
AAAAATAATTATATGAATTTTTTTTATAA
Found at i:18897613 original size:30 final size:29
Alignment explanation
Indices: 18897579--18897645 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 29
18897569 TTTTTATACT
*
18897579 TGAAATTATCAAAGATTTAAT-TTTAATTAA
1 TGAAATTAT-AAA-ATTTAATATTTAATCAA
*
18897609 TGAAATTA-AAAATTTAATATTTTATCAA
1 TGAAATTATAAAATTTAATATTTAATCAA
18897637 T-AAATTATA
1 TGAAATTATA
18897646 CGATTATTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 13 0.39
28 12 0.36
30 8 0.24
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (29 bp):
TGAAATTATAAAATTTAATATTTAATCAA
Found at i:18898710 original size:2 final size:2
Alignment explanation
Indices: 18898705--18898735 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18898695 TCTCTCTCTC
*
18898705 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18898736 GAATGTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18900994 original size:61 final size:61
Alignment explanation
Indices: 18900899--18901022 Score: 194
Period size: 61 Copynumber: 2.0 Consensus size: 61
18900889 TTTCAGTTAT
* * * *
18900899 TATTCTTGTCTGTGATGAGGTTCTAATTTAACATCCAAATCACATGTACTAAATTTATCCC
1 TATTCGTGTCTGTGATGAGGTTCTAATATAACATCCAAATCACATATACCAAATTTATCCC
* *
18900960 TATTCGTGTCTGTGATGATGTTCTAATATAACATCCAAATCACATATACCAAATTTGTCCC
1 TATTCGTGTCTGTGATGAGGTTCTAATATAACATCCAAATCACATATACCAAATTTATCCC
18901021 TA
1 TA
18901023 ACTGCTTAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (61 bp):
TATTCGTGTCTGTGATGAGGTTCTAATATAACATCCAAATCACATATACCAAATTTATCCC
Found at i:18902536 original size:52 final size:51
Alignment explanation
Indices: 18902470--18902626 Score: 215
Period size: 52 Copynumber: 3.0 Consensus size: 51
18902460 TGAACAAGAA
* *
18902470 GACTTGCAAAAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAAG-GGATTCTTAATAGGCAAGTTT
* *
18902522 GACTTGCAAGAGAAGAGTTCTAAAAAGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCT-AAGAGAAAGGGATTCTTAATAGGCAAGTTT
* ** *
18902574 GACTTACAAGAGAAGAATTCTAAGAGGAGTGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGA-GAAAGGGATTCTTAATAGGCAAGTTT
18902626 G
1 G
18902627 TATGGTTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 3 0.03
52 82 0.88
53 8 0.09
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.26
Consensus pattern (51 bp):
GACTTGCAAGAGAAGAATTCTAAGAGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:18903146 original size:30 final size:31
Alignment explanation
Indices: 18903110--18903194 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 31
18903100 GAGGCTTTTA
*
18903110 GCCCAACAAATGATATCAGAGCTGTGATG-T
1 GCCCAACAAATGGTATCAGAGCTGTGATGTT
*
18903140 GCCCAACAAATGGTATCAGAGCTGTGGTGTT
1 GCCCAACAAATGGTATCAGAGCTGTGATGTT
* * *
18903171 CCCCAACAAGTGGTATCATAGCTG
1 GCCCAACAAATGGTATCAGAGCTG
18903195 AAAGTTCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 27 0.55
31 22 0.45
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (31 bp):
GCCCAACAAATGGTATCAGAGCTGTGATGTT
Found at i:18903547 original size:11 final size:11
Alignment explanation
Indices: 18903531--18903572 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
18903521 AATCCCATAA
18903531 GAGATTTGTTT
1 GAGATTTGTTT
*
18903542 GAGATTTGTTA
1 GAGATTTGTTT
18903553 GAGATTTGTTT
1 GAGATTTGTTT
18903564 GAGATTTGT
1 GAGATTTGT
18903573 CAGATATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:18903558 original size:22 final size:22
Alignment explanation
Indices: 18903530--18903572 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
18903520 AAATCCCATA
18903530 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
18903552 AGAGATTTGTTTGAGATTTGT
1 AGAGATTTGTTTGAGATTTGT
18903573 CAGATATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:18903684 original size:52 final size:52
Alignment explanation
Indices: 18903597--18903753 Score: 235
Period size: 52 Copynumber: 3.0 Consensus size: 52
18903587 TGGACAAGAA
* * *
18903597 GACTTGCAAAAGAAAAATTCTAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTT
*
18903649 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
* * *
18903701 GACTTACAAGAGAAGAATTCTAAGAGAAAAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
18903753 G
1 G
18903754 TATGGTTATA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
52 91 0.95
53 5 0.05
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:18913291 original size:2 final size:2
Alignment explanation
Indices: 18913284--18913311 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18913274 CATTTTCGAT
18913284 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
18913312 AGCAAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:18916844 original size:24 final size:24
Alignment explanation
Indices: 18916812--18916860 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
18916802 CTCTAGCTTT
* *
18916812 GTCGACTTTTCTTCCCATCTCACA
1 GTCGACTTTTCTTACCATATCACA
18916836 GTCGACTTTTCTTACCATATCACA
1 GTCGACTTTTCTTACCATATCACA
18916860 G
1 G
18916861 CAGAGCCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (24 bp):
GTCGACTTTTCTTACCATATCACA
Found at i:18927745 original size:15 final size:15
Alignment explanation
Indices: 18927721--18927753 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
18927711 ATTTACTTGG
18927721 TTTTTTTTTTTTC-T
1 TTTTTTTTTTTTCAT
18927735 TTTTTTCTTTTTTCAT
1 TTTTTT-TTTTTTCAT
18927751 TTT
1 TTT
18927754 ACACAAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTCAT
Found at i:18927831 original size:7 final size:7
Alignment explanation
Indices: 18927819--18927844 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18927809 TCAAAGCAAC
18927819 TTCTGAG
1 TTCTGAG
18927826 TTCTGAG
1 TTCTGAG
18927833 TTCTGAG
1 TTCTGAG
18927840 TTCTG
1 TTCTG
18927845 TCCTTTGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.46
Consensus pattern (7 bp):
TTCTGAG
Found at i:18936716 original size:42 final size:42
Alignment explanation
Indices: 18936649--18936738 Score: 137
Period size: 42 Copynumber: 2.1 Consensus size: 42
18936639 GAAATTATAA
*
18936649 ATTTCATTTCAAGTTATTAGAGTTTTTAATTTAATA-TTTTGAT
1 ATTT-ATTTCAAGTTATTAGAGTTTTAAATTTAATATTTTTG-T
*
18936692 ATTTATTTCAAGTTATTAGGGTTTTAAATTTAATATTTTTGT
1 ATTTATTTCAAGTTATTAGAGTTTTAAATTTAATATTTTTGT
18936734 ATTTA
1 ATTTA
18936739 AATATTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 35 0.80
43 9 0.20
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (42 bp):
ATTTATTTCAAGTTATTAGAGTTTTAAATTTAATATTTTTGT
Found at i:18936932 original size:28 final size:27
Alignment explanation
Indices: 18936891--18936944 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
18936881 ATTAAATTTT
* *
18936891 AAAATTAAAAAATTTGATTTAATTAAA
1 AAAAATAAAAAATTTAATTTAATTAAA
*
18936918 AAAAATAAAATAATTTAATTTCATTAA
1 AAAAATAAAA-AATTTAATTTAATTAA
18936945 TTCGATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
AAAAATAAAAAATTTAATTTAATTAAA
Found at i:18937830 original size:14 final size:15
Alignment explanation
Indices: 18937806--18937834 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18937796 TGAGAATTTT
18937806 TTTATAAAAATATAA
1 TTTATAAAAATATAA
18937821 TTTA-AAAAATATAA
1 TTTATAAAAATATAA
18937835 AAAATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTATAAAAATATAA
Found at i:18939814 original size:21 final size:21
Alignment explanation
Indices: 18939771--18939824 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
18939761 AAAAACCATG
* *
18939771 CTTCTCCATCTTCTTCACGGT
1 CTTCTACATCATCTTCACGGT
18939792 CTTCTACATCATCTTCATC-GT
1 CTTCTACATCATCTTCA-CGGT
18939813 CTT-TATCATCAT
1 CTTCTA-CATCAT
18939825 GGTTATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.17, C:0.33, G:0.06, T:0.44
Consensus pattern (21 bp):
CTTCTACATCATCTTCACGGT
Found at i:18941662 original size:8 final size:8
Alignment explanation
Indices: 18941640--18941704 Score: 76
Period size: 8 Copynumber: 7.8 Consensus size: 8
18941630 CAAAGGAGCT
18941640 TGTATTATA
1 TGTA-TATA
*
18941649 TATATATA
1 TGTATATA
18941657 TGTATATGTA
1 TGTATA--TA
18941667 TGTATATA
1 TGTATATA
18941675 TGTATATA
1 TGTATATA
*
18941683 TGTATGTA
1 TGTATATA
*
18941691 TGTATGTA
1 TGTATATA
18941699 TGTATA
1 TGTATA
18941705 AAGTAAGAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
8 39 0.78
9 3 0.06
10 8 0.16
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (8 bp):
TGTATATA
Found at i:18941674 original size:12 final size:12
Alignment explanation
Indices: 18941640--18941704 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
18941630 CAAAGGAGCT
18941640 TGTAT-TATATA
1 TGTATATATATA
* *
18941651 TATATATGTATA
1 TGTATATATATA
*
18941663 TGTATGTATATA
1 TGTATATATATA
*
18941675 TGTATATATGTA
1 TGTATATATATA
* *
18941687 TGTATGTATGTA
1 TGTATATATATA
18941699 TGTATA
1 TGTATA
18941705 AAGTAAGAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 4 0.09
12 40 0.91
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (12 bp):
TGTATATATATA
Found at i:18941688 original size:4 final size:4
Alignment explanation
Indices: 18941661--18941703 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
18941651 TATATATGTA
* *
18941661 TATG TATG TATA TATG TATA TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
18941704 AAAGTAAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:18945439 original size:11 final size:13
Alignment explanation
Indices: 18945404--18945432 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18945394 TTTATTGTTT
18945404 TTTTAATATATTA
1 TTTTAATATATTA
18945417 TTTTAATATATTA
1 TTTTAATATATTA
18945430 TTT
1 TTT
18945433 ATATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTAATATATTA
Done.